def test_classify_paired_reads(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
#Non chimeric
query1 = '>seq1 1:N:0:GATCAG\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT\n'
query2 = '>seq1 2:N:0:GATCAG\nAGGAGGGATCGGGCACCCACGGCGCGGTAGACTGAGGCCTTCTCGAACT\n'
#Chimeric
query3 = '>seq2 1:N:0:GATCAG\nAAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGTCTGCGATCCC\n'
query4 = '>seq2 2:N:0:GATCAG\nACGTGGATGCGGCGACGGCCCTACGGCACATACTGTTATTAGGGTCACT\n'
#unknown
query5 = '>seq3 1:N:0:GATCAG\nAGTGACCCTAATAACAGTATGTGCCGTAGGGCCGTCGCCGCATCCACGT\n'
query6 = '>seq3 2:N:0:GATCAG\nGTCGTGCGCAGCCATTGAGACCTTCCTAGGGTTTTCCCCATGGAATCGG\n'
query = query1 + query2 + query5 + query6 + query3 + query4
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
bam_fhand = NamedTemporaryFile(suffix='.bam')
extra_params = ['-a', '-M']
bwa = map_with_bwamem(index_fpath, interleave_fpath=in_fhand.name,
extra_params=extra_params)
map_process_to_sortedbam(bwa, bam_fhand.name, key='queryname')
result = classify_mapped_reads(bam_fhand, mate_distance=2000)
for pair, kind in result:
if kind == NON_CHIMERIC:
assert 'seq1' in get_name(pair[0])
elif kind == UNKNOWN:
assert 'seq3' in get_name(pair[0])
elif kind == CHIMERA:
assert 'seq2' in get_name(pair[0])
else:
self.fail()
def test_giuseppe_reads():
'It splits some real reads'
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
new_seqs = []
for packet in read_seq_packets([open(seq_fpath)], 2):
new_seqs.extend(splitter(packet))
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01BJHT8\\1' in seq_names
assert 'G109AZL01BJHT8\\2' in seq_names
assert len(new_seqs) == 20
# test with process_seq_packet
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
seq_packets = read_seq_packets([open(seq_fpath)], 2)
seq_packets = process_seq_packets(seq_packets, [splitter])[0]
new_seqs = [seq for l in list(seq_packets) for seq in l]
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01BJHT8\\1' in seq_names
assert 'G109AZL01BJHT8\\2' in seq_names
assert len(new_seqs) == 20
# reads 2
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads2.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
new_seqs = []
for packet in read_seq_packets([open(seq_fpath)], 2):
new_seqs.extend(splitter(packet))
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01D8U3X\\1' in seq_names
assert 'G109AZL01D8U3X\\2' in seq_names
assert len(new_seqs) == 20
# test with process_seq_packet
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads2.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
seq_packets = read_seq_packets([open(seq_fpath)], 2)
seq_packets = process_seq_packets(seq_packets, [splitter])[0]
new_seqs = [seq for l in list(seq_packets) for seq in l]
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01D8U3X\\1' in seq_names
assert 'G109AZL01D8U3X\\2' in seq_names
assert len(new_seqs) == 20
def test_giuseppe_reads():
'It splits some real reads'
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
new_seqs = []
for packet in read_seq_packets([open(seq_fpath)], 2):
new_seqs.extend(splitter(packet))
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01BJHT8\\1' in seq_names
assert 'G109AZL01BJHT8\\2' in seq_names
assert len(new_seqs) == 20
# test with process_seq_packet
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
seq_packets = read_seq_packets([open(seq_fpath)], 2)
seq_packets = process_seq_packets(seq_packets, [splitter])[0]
new_seqs = [seq for l in list(seq_packets) for seq in l]
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01BJHT8\\1' in seq_names
assert 'G109AZL01BJHT8\\2' in seq_names
assert len(new_seqs) == 20
# reads 2
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads2.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
new_seqs = []
for packet in read_seq_packets([open(seq_fpath)], 2):
new_seqs.extend(splitter(packet))
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01D8U3X\\1' in seq_names
assert 'G109AZL01D8U3X\\2' in seq_names
assert len(new_seqs) == 20
# test with process_seq_packet
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads2.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
seq_packets = read_seq_packets([open(seq_fpath)], 2)
seq_packets = process_seq_packets(seq_packets, [splitter])[0]
new_seqs = [seq for l in list(seq_packets) for seq in l]
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01D8U3X\\1' in seq_names
assert 'G109AZL01D8U3X\\2' in seq_names
assert len(new_seqs) == 20
def test_sort_by_position_in_ref(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
#with fasta format
query1 = '>seq1\nGAGAATTAAGCCTATCTGGAGAGCGGTACCAACAGGGAAACACCGACTCA\n'
query2 = '>seq2\nTAACAGTATGTGCCGTAGGGCCGTCGCCGCATCCACGTTATCGGAAGGGC\n'
query3 = '>seq3\nTACGGCCGTCCCCCTGCTGCTTATCATCAGGCGACGATAGTCAGCTCCGC\n'
query4 = '>seq4\nTGCAGAGACCGACATGCGAAAGGAGTGACTATCACCGTCAATGGCGTGCC\n'
query5 = '>seq5\nAATAAATAATCTGGGTATGTACTCGGAGTCTACGTAAGCGCGCTTAAATT\n'
query6 = '>seq6\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files(in_fhand, 'coordinate', index_fpath):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#it fails because bwa somehow gives a position to an unmapped seq
#with fastq format
query1 += '+\n??????????????????????????????????????????????????\n'
query2 += '+\n??????????????????????????????????????????????????\n'
query3 += '+\n??????????????????????????????????????????????????\n'
query4 += '+\n??????????????????????????????????????????????????\n'
query5 += '+\n??????????????????????????????????????????????????\n'
query6 += '+\n??????????????????????????????????????????????????\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files(in_fhand, 'coordinate', index_fpath):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#sort by sequence
sorted_names = []
for seq in sort_fastx_files([in_fhand],
key='seq',
directory=None,
max_items_in_memory=None,
tempdir=None):
sorted_names.append(get_name(seq))
expected_names = ['seq6', 'seq5', 'seq1', 'seq2', 'seq3', 'seq4']
assert sorted_names == expected_names
def test_sort_by_position_in_ref(self):
reference = GENOME
ref_fhand = NamedTemporaryFile()
ref_fhand.write(reference)
ref_fhand.flush()
#with fasta format
query1 = '>seq1\nGAGAATTAAGCCTATCTGGAGAGCGGTACCAACAGGGAAACACCGACTCA\n'
query2 = '>seq2\nTAACAGTATGTGCCGTAGGGCCGTCGCCGCATCCACGTTATCGGAAGGGC\n'
query3 = '>seq3\nTACGGCCGTCCCCCTGCTGCTTATCATCAGGCGACGATAGTCAGCTCCGC\n'
query4 = '>seq4\nTGCAGAGACCGACATGCGAAAGGAGTGACTATCACCGTCAATGGCGTGCC\n'
query5 = '>seq5\nAATAAATAATCTGGGTATGTACTCGGAGTCTACGTAAGCGCGCTTAAATT\n'
query6 = '>seq6\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files([in_fhand], 'coordinate', ref_fhand.name):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#with fastq format
query1 += '+\n??????????????????????????????????????????????????\n'
query2 += '+\n??????????????????????????????????????????????????\n'
query3 += '+\n??????????????????????????????????????????????????\n'
query4 += '+\n??????????????????????????????????????????????????\n'
query5 += '+\n??????????????????????????????????????????????????\n'
query6 += '+\n??????????????????????????????????????????????????\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files([in_fhand], 'coordinate', ref_fhand.name):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#sort by sequence
sorted_names = []
for seq in sort_fastx_files([in_fhand], key='seq', directory=None,
max_items_in_memory=None, tempdir=None):
sorted_names.append(get_name(seq))
expected_names = ['seq6', 'seq5', 'seq1', 'seq2', 'seq3', 'seq4']
assert sorted_names == expected_names
def __call__(self, seqs):
'It splits a list of sequences with the provided linkers'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
min_identity = 87.0
min_len = 13
filters = [{'kind': 'min_length', 'min_num_residues': min_len,
'length_in_query': False, 'filter_match_parts': True},
{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': min_identity}]
matcher = BlasterForFewSubjects(seq_fhand.name, self.linkers,
program='blastn', filters=filters,
params={'task': 'blastn-short'},
elongate_for_global=True,
seqs_type=NUCL)
new_seqs = []
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
split_seqs = self._split_by_mate_linker(seq, segments)
else:
split_seqs = [seq]
for seq in split_seqs:
new_seqs.append(seq)
return new_seqs
def test_many_reads(self):
'It splits lots of reads to check that blast finds everything'
linker = TITANIUM_LINKER
def create_seq(index):
'It creates a random seq with a linker'
seq1 = ''.join(choice('ACTG') for i in range(100))
seq2 = ''.join(choice('ACTG') for i in range(100))
seq = seq1 + linker + seq2
seq = SeqRecord(id='seq_' + str(index), seq=Seq(seq))
seq = SeqWrapper(SEQRECORD, seq, None)
return seq
# We want to test that blast reports all reads
packet_size = get_setting('PACKET_SIZE')
default_blast_max_target_size = 500
assert packet_size > default_blast_max_target_size
seqs = [create_seq(i) for i in range(1000)]
splitter = MatePairSplitter()
for index, seq in enumerate(splitter(seqs)):
seq_index = index // 2
pair_index = (index % 2) + 1
expected_id = 'seq_' + str(seq_index) + '\\' + str(pair_index)
assert get_name(seq) == expected_id
def __call__(self, seqs):
'It runs the actual annotations'
if not seqs:
return seqs
pep_fhand = NamedTemporaryFile()
dna_fhand = NamedTemporaryFile()
_run_estscan(seqs, pep_fhand.name, dna_fhand.name,
self._usage_matrix)
# now we read the result files
estscan_result = _read_estcan_results(open(pep_fhand.name),
open(dna_fhand.name))
for seq in seqs:
seq_name = get_name(seq)
orfs = estscan_result.get(seq_name, {})
feats = []
for (start, end, strand), str_seqs in orfs.viewitems():
start -= 1
# end is fine -- end[
feat = SeqFeature(location=FeatureLocation(start, end, strand),
type='ORF', qualifiers=str_seqs)
feats.append(feat)
if feats:
seq.object.features.extend(feats)
dna_fhand.close()
pep_fhand.close()
return seqs
def match_pairs(
reads,
out_fhand,
orphan_out_fhand,
out_format,
ordered=True,
check_order_buffer_size=0,
max_reads_memory=None,
temp_dir=None,
):
"""It matches the seq pairs in an iterator and splits the orphan seqs."""
counts = 0
check_order_buffer = KeyedSet()
for pair in _get_paired_and_orphan(reads, ordered, max_reads_memory, temp_dir):
if len(pair) == 1:
write_seqs(pair, orphan_out_fhand, out_format)
try:
name = _parse_pair_direction_and_name(pair[0])[0]
except PairDirectionError:
name = get_name(pair[0])
if ordered and counts < check_order_buffer_size:
counts += 1
if not check_order_buffer.check_add(name):
msg = "Reads are not ordered by pairs.Use unordered option"
raise ItemsNotSortedError(msg)
elif ordered and counts >= check_order_buffer_size:
if name in check_order_buffer:
msg = "Reads are not ordered by pairs.Use unordered option"
raise ItemsNotSortedError(msg)
elif len(pair) == 2:
write_seqs(pair, out_fhand, out_format)
flush_fhand(orphan_out_fhand)
flush_fhand(out_fhand)
def __call__(self, seqs):
'It runs the actual annotations'
if not seqs:
return seqs
pep_fhand = NamedTemporaryFile()
dna_fhand = NamedTemporaryFile()
_run_estscan(seqs, pep_fhand.name, dna_fhand.name,
self._usage_matrix)
# now we read the result files
estscan_result = _read_estcan_results(open(pep_fhand.name),
open(dna_fhand.name))
for seq in seqs:
seq_name = get_name(seq)
orfs = estscan_result.get(seq_name, {})
feats = []
for (start, end, strand), str_seqs in orfs.viewitems():
start -= 1
# end is fine -- end[
feat = SeqFeature(location=FeatureLocation(start, end, strand),
type='ORF', qualifiers=str_seqs)
feats.append(feat)
if feats:
seq.object.features.extend(feats)
dna_fhand.close()
pep_fhand.close()
return seqs
def __call__(self, seqs):
'It splits a list of sequences with the provided linkers'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
min_identity = 87.0
min_len = 13
filters = [{'kind': 'min_length', 'min_num_residues': min_len,
'length_in_query': False, 'filter_match_parts': True},
{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': min_identity}]
matcher = BlasterForFewSubjects(seq_fhand.name, self.linkers,
program='blastn', filters=filters,
params={'task': 'blastn-short'},
elongate_for_global=True,
seqs_type=NUCL)
new_seqs = []
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
split_seqs = self._split_by_mate_linker(seq, segments)
else:
split_seqs = [seq]
for seq in split_seqs:
new_seqs.append(seq)
return new_seqs
def append_to_description(seqrecord, text):
'it appends the text to the seqrecord description'
desc = get_description(seqrecord)
if desc in (None, get_name(seqrecord), '<unknown description>'):
desc = ''
desc += text
seqrecord.object.description = desc
def test_many_reads(self):
'It splits lots of reads to check that blast finds everything'
linker = TITANIUM_LINKER
def create_seq(index):
'It creates a random seq with a linker'
seq1 = ''.join(choice('ACTG') for i in range(100))
seq2 = ''.join(choice('ACTG') for i in range(100))
seq = seq1 + linker + seq2
seq = SeqRecord(id='seq_' + str(index), seq=Seq(seq))
seq = SeqWrapper(SEQRECORD, seq, None)
return seq
# We want to test that blast reports all reads
packet_size = get_setting('PACKET_SIZE')
default_blast_max_target_size = 500
assert packet_size > default_blast_max_target_size
seqs = [create_seq(i) for i in range(1000)]
splitter = MatePairSplitter()
for index, seq in enumerate(splitter(seqs)):
seq_index = index // 2
pair_index = (index % 2) + 1
expected_id = 'seq_' + str(seq_index) + '\\' + str(pair_index)
assert get_name(seq) == expected_id
def append_to_description(seqrecord, text):
'it appends the text to the seqrecord description'
desc = get_description(seqrecord)
if desc in (None, get_name(seqrecord), '<unknown description>'):
desc = ''
desc += text
seqrecord.object.description = desc
def match_pairs(reads,
out_fhand,
orphan_out_fhand,
out_format,
ordered=True,
check_order_buffer_size=0,
max_reads_memory=None,
temp_dir=None):
'''It matches the seq pairs in an iterator and splits the orphan seqs.'''
counts = 0
check_order_buffer = KeyedSet()
for pair in _get_paired_and_orphan(reads, ordered, max_reads_memory,
temp_dir):
if len(pair) == 1:
write_seqs(pair, orphan_out_fhand, out_format)
try:
name = _parse_pair_direction_and_name(pair[0])[0]
except PairDirectionError:
name = get_name(pair[0])
if ordered and counts < check_order_buffer_size:
counts += 1
if not check_order_buffer.check_add(name):
msg = 'Reads are not ordered by pairs.Use unordered option'
raise ItemsNotSortedError(msg)
elif ordered and counts >= check_order_buffer_size:
if name in check_order_buffer:
msg = 'Reads are not ordered by pairs.Use unordered option'
raise ItemsNotSortedError(msg)
elif len(pair) == 2:
write_seqs(pair, out_fhand, out_format)
flush_fhand(orphan_out_fhand)
flush_fhand(out_fhand)
def test_sort_by_position_in_ref(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
#with fasta format
query1 = '>seq1\nGAGAATTAAGCCTATCTGGAGAGCGGTACCAACAGGGAAACACCGACTCA\n'
query2 = '>seq2\nTAACAGTATGTGCCGTAGGGCCGTCGCCGCATCCACGTTATCGGAAGGGC\n'
query3 = '>seq3\nTACGGCCGTCCCCCTGCTGCTTATCATCAGGCGACGATAGTCAGCTCCGC\n'
query4 = '>seq4\nTGCAGAGACCGACATGCGAAAGGAGTGACTATCACCGTCAATGGCGTGCC\n'
query5 = '>seq5\nAATAAATAATCTGGGTATGTACTCGGAGTCTACGTAAGCGCGCTTAAATT\n'
query6 = '>seq6\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files(in_fhand, 'coordinate', index_fpath):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#it fails because bwa somehow gives a position to an unmapped seq
#with fastq format
query1 += '+\n??????????????????????????????????????????????????\n'
query2 += '+\n??????????????????????????????????????????????????\n'
query3 += '+\n??????????????????????????????????????????????????\n'
query4 += '+\n??????????????????????????????????????????????????\n'
query5 += '+\n??????????????????????????????????????????????????\n'
query6 += '+\n??????????????????????????????????????????????????\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files(in_fhand, 'coordinate', index_fpath):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#sort by sequence
sorted_names = []
for seq in sort_fastx_files([in_fhand], key='seq', directory=None,
max_items_in_memory=None, tempdir=None):
sorted_names.append(get_name(seq))
expected_names = ['seq6', 'seq5', 'seq1', 'seq2', 'seq3', 'seq4']
assert sorted_names == expected_names
def test_filter_chimeras(self):
reference_seq = GENOME
#Typic non chimeric
query1 = '>seq1 1:Y:18:ATCACG\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTA'
query1 += 'CATTGAACTT\n'
query2 = '>seq1 2:Y:18:ATCACG\nCATCATTGCATAAGTAACACTCAACCAACAGTGCTACAG'
query2 += 'GGTTGTAACG\n'
#typic chimeric
query3 = '>seq2 1:Y:18:ATCACG\nAAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGT'
query3 += 'CTGCGATCCCTG'
query3 += 'GGTAGACTGAGGCCTTCTCGAACTACAAATCATCACCAGACCATGTCCGA\n'
query4 = '>seq2 2:Y:18:ATCACG\nTTAAGGCACGTACGGTACCTAAATCGGCCTGATGGTATT'
query4 += 'GATGCTGAACTT'
query4 += 'ATTGCGGCTCACACACCCCTACGTTACACGCAAATGCTGCCCGAAACGTTAT\n'
#Unknown, 3' end does not map, impossible to know if it is chimeric
query13 = '>seq7 1:Y:18:ATCACG\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCT'
query13 += 'ACATTGAACTT'
query13 += 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query14 = '>seq7 2:Y:18:ATCACG\nATCATTGCATAAGTAACACTCAACCAACAGTGCTACAG'
query14 += 'GGTTGTAACGCC'
query14 += 'CCTCGAAGGTACCTTTGCCAGACTGGGCTACAGGACACCCAGTCTCCCGGGAGTCT\n'
query = query1 + query2 + query3 + query4 + query13 + query14
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
ref_fhand = NamedTemporaryFile()
ref_fhand.write(reference_seq)
ref_fhand.flush()
out_fhand = NamedTemporaryFile()
chimeras_fhand = NamedTemporaryFile()
unknown_fhand = NamedTemporaryFile()
filter_chimeras(ref_fhand.name, out_fhand, chimeras_fhand, [in_fhand],
unknown_fhand)
result = read_seqs([out_fhand])
chimeric = read_seqs([chimeras_fhand])
unknown = read_seqs([unknown_fhand])
for seq in result:
assert get_name(seq) in ['seq1.f', 'seq1.r']
for seq in chimeric:
assert get_name(seq) in ['seq2.f', 'seq2.r']
for seq in unknown:
assert get_name(seq) in ['seq7.f', 'seq7.r']
def _do_check(self, seq):
count = self._read_counts[get_name(seq)]
kb_len = count['length'] / 1000
rpk = count['mapped_reads'] / kb_len # rpks
rpkm = rpk / self._million_reads # rpkms
return True if rpkm >= self._min_rpkm else False
def _do_check(self, seq):
count = self._read_counts[get_name(seq)]
kb_len = count['length'] / 1000
rpk = count['mapped_reads'] / kb_len # rpks
rpkm = rpk / self._million_reads # rpkms
return True if rpkm >= self._min_rpkm else False
def test_trim_seqs():
'It tests the trim seq function'
seqs = []
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('aaCTTTC')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('CTTCaa')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('aaCTCaa')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('actg')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('AC')), None)])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CTTTC', 'CTTC', 'CTC', 'AC']
seqs = []
seq = SeqItem('s', ['>s\n', 'aaCTTTC\n'])
seqs.append([SeqWrapper(SEQITEM, seq, 'fasta')])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CTTTC']
# with pairs
seq = SeqItem('s.f', ['>s.f\n', 'aaCTTTC\n'])
seq1 = SeqItem('s.r', ['>s.r\n', 'aaCTTTC\n'])
seq2 = SeqItem('s1.f', ['>s1.f\n', 'aa\n'])
seq3 = SeqItem('s1.r', ['>s1.r\n', 'aaCTTTC\n'])
seqs = []
seqs.append([SeqWrapper(SEQITEM, seq, 'fasta'),
SeqWrapper(SEQITEM, seq1, 'fasta')])
seqs.append([SeqWrapper(SEQITEM, seq2, 'fasta'),
SeqWrapper(SEQITEM, seq3, 'fasta')])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
orphan_res = [get_str_seq(s) for s in trim_packet[ORPHAN_SEQS]]
assert orphan_res == ['CTTTC']
assert ['CTTTC', 'CTTTC'] == res
# no drag
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
orphan_res = [get_name(s) for s in trim_packet[ORPHAN_SEQS]]
assert orphan_res == ['s1.r']
assert ['CTTTC', 'CTTTC'] == res
def test_trim_seqs():
'It tests the trim seq function'
seqs = []
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('aaCTTTC')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('CTTCaa')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('aaCTCaa')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('actg')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('AC')), None)])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CTTTC', 'CTTC', 'CTC', 'AC']
seqs = []
seq = SeqItem('s', ['>s\n', 'aaCTTTC\n'])
seqs.append([SeqWrapper(SEQITEM, seq, 'fasta')])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CTTTC']
# with pairs
seq = SeqItem('s.f', ['>s.f\n', 'aaCTTTC\n'])
seq1 = SeqItem('s.r', ['>s.r\n', 'aaCTTTC\n'])
seq2 = SeqItem('s1.f', ['>s1.f\n', 'aa\n'])
seq3 = SeqItem('s1.r', ['>s1.r\n', 'aaCTTTC\n'])
seqs = []
seqs.append([SeqWrapper(SEQITEM, seq, 'fasta'),
SeqWrapper(SEQITEM, seq1, 'fasta')])
seqs.append([SeqWrapper(SEQITEM, seq2, 'fasta'),
SeqWrapper(SEQITEM, seq3, 'fasta')])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
orphan_res = [get_str_seq(s) for s in trim_packet[ORPHAN_SEQS]]
assert orphan_res == ['CTTTC']
assert ['CTTTC', 'CTTTC'] == res
# no drag
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
orphan_res = [get_name(s) for s in trim_packet[ORPHAN_SEQS]]
assert orphan_res == ['s1.r']
assert ['CTTTC', 'CTTTC'] == res
def test_split_mate(self):
'It tests the function that splits seqs using segments'
# pylint: disable=W0212
seq = 'aaatttccctt'
seq = SeqWrapper(SEQRECORD, SeqRecord(Seq(seq), id='seq'), None)
# fake class to test
splitter = MatePairSplitter([seq])
# segment beginning
seqs = splitter._split_by_mate_linker(seq, ([(0, 3)], False))
assert get_str_seq(seqs[0]) == 'ttccctt'
assert get_name(seqs[0]) == 'seq'
# segment at end
seqs = splitter._split_by_mate_linker(seq, ([(7, 11)], False))
assert get_str_seq(seqs[0]) == 'aaatttc'
assert get_name(seqs[0]) == 'seq'
# segmnent in the middle
seqs = splitter._split_by_mate_linker(seq, ([(4, 7)], True))
assert get_str_seq(seqs[0]) == 'aaat'
assert get_str_seq(seqs[1]) == 'ctt'
assert get_name(seqs[0]) == 'seq_pl.part1'
assert get_name(seqs[1]) == 'seq_pl.part2'
seqs = splitter._split_by_mate_linker(seq, ([(4, 7)], False))
assert get_name(seqs[0]) == r'seq\1'
assert get_name(seqs[1]) == r'seq\2'
seqs = splitter._split_by_mate_linker(seq, ([(4, 6), (8, 9)],
False))
assert get_str_seq(seqs[0]) == 'aaat'
assert get_str_seq(seqs[1]) == 'c'
assert get_str_seq(seqs[2]) == 't'
assert get_name(seqs[0]) == 'seq_mlc.part1'
# all sequence is linker
seqs = splitter._split_by_mate_linker(seq, ([(0, 10)], False))
assert not get_str_seq(seqs[0])
# there's no segments
seqs = splitter._split_by_mate_linker(seq, ([], False))
assert get_name(seq) == get_name(seqs[0])
assert get_str_seq(seq) == get_str_seq(seqs[0])
def __call__(self, seqrecords):
'It does the work'
if not seqrecords:
return seqrecords
matcher = Blaster(seqrecords,
self.blastdb,
self._program,
self._dbtype,
filters=self._filters,
params=self._params,
remote=self._remote)
blasts = matcher.blasts
blastdb = os.path.basename(self.blastdb)
for seqrecord in seqrecords:
align_result = blasts.get(get_name(seqrecord), None)
if not align_result:
continue
match_counter = 0
for match in align_result['matches']:
subject = match['subject']['name']
match_counter += 1
for match_part in match['match_parts']:
if match_part['subject_end'] < match_part['subject_start']:
strand = -1
subject_start = match_part['subject_end']
subject_end = match_part['subject_start']
else:
strand = 1
subject_start = match_part['subject_start']
subject_end = match_part['subject_end']
query_start = match_part['query_start']
query_end = match_part['query_end']
qualifiers = {}
qualifiers['Target'] = {
'start': subject_start,
'end': subject_end,
'name': subject
}
qualifiers['score'] = match_part['scores']['expect']
qualifiers['identity'] = match_part['scores']['identity']
qualifiers['blastdb'] = blastdb
location = FeatureLocation(query_start, query_end, strand)
feature = SeqFeature(
location=location,
type='match_part',
qualifiers=qualifiers,
id='match{0:03d}'.format(match_counter))
seqrecord.object.features.append(feature)
return seqrecords
def test_blastmatch_filter():
'it test filter by blast'
seq = 'CCAAAGTACGGTCTCCCAAGCGGTCTCTTACCGGACACCGTCACCGATTTCACCCTCT'
oligo = 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
seq_oligo = seq + oligo
oligo = SeqRecord(Seq(oligo))
oligo = SeqWrapper(SEQRECORD, oligo, None)
seq = SeqRecord(Seq(seq), id='seq')
seq = SeqWrapper(object=seq, kind=SEQRECORD, file_format=None)
seq_oligo = SeqRecord(Seq(seq_oligo), id='seq_oligo')
seq_oligo = SeqWrapper(object=seq_oligo, kind=SEQRECORD,
file_format=None)
seqs = {SEQS_PASSED: [[seq], [seq_oligo]], SEQS_FILTERED_OUT: []}
filter_ = FilterBlastShort([oligo])
filt_packet = filter_(seqs)
passed = [get_name(pair[0]) for pair in filt_packet[SEQS_PASSED]]
fail = [get_name(pair[0]) for pair in filt_packet[SEQS_FILTERED_OUT]]
assert passed == ['seq']
assert fail == ['seq_oligo']
def test_split_mate(self):
'It tests the function that splits seqs using segments'
# pylint: disable=W0212
seq = 'aaatttccctt'
seq = SeqWrapper(SEQRECORD, SeqRecord(Seq(seq), id='seq'), None)
# fake class to test
splitter = MatePairSplitter([seq])
# segment beginning
seqs = splitter._split_by_mate_linker(seq, ([(0, 3)], False))
assert get_str_seq(seqs[0]) == 'ttccctt'
assert get_name(seqs[0]) == 'seq'
# segment at end
seqs = splitter._split_by_mate_linker(seq, ([(7, 11)], False))
assert get_str_seq(seqs[0]) == 'aaatttc'
assert get_name(seqs[0]) == 'seq'
# segmnent in the middle
seqs = splitter._split_by_mate_linker(seq, ([(4, 7)], True))
assert get_str_seq(seqs[0]) == 'aaat'
assert get_str_seq(seqs[1]) == 'ctt'
assert get_name(seqs[0]) == 'seq_pl.part1'
assert get_name(seqs[1]) == 'seq_pl.part2'
seqs = splitter._split_by_mate_linker(seq, ([(4, 7)], False))
assert get_name(seqs[0]) == r'seq\1'
assert get_name(seqs[1]) == r'seq\2'
seqs = splitter._split_by_mate_linker(seq, ([(4, 6), (8, 9)], False))
assert get_str_seq(seqs[0]) == 'aaat'
assert get_str_seq(seqs[1]) == 'c'
assert get_str_seq(seqs[2]) == 't'
assert get_name(seqs[0]) == 'seq_mlc.part1'
# all sequence is linker
seqs = splitter._split_by_mate_linker(seq, ([(0, 10)], False))
assert not get_str_seq(seqs[0])
# there's no segments
seqs = splitter._split_by_mate_linker(seq, ([], False))
assert get_name(seq) == get_name(seqs[0])
assert get_str_seq(seq) == get_str_seq(seqs[0])
def _do_check(self, seq):
seq_object = seq.object
try:
quals = seq_object.letter_annotations['phred_quality']
except KeyError:
msg = 'Some of the input sequences do not have qualities: {}'
msg = msg.format(get_name(seq))
raise WrongFormatError(msg)
if self.ignore_masked:
str_seq = str(seq_object.seq)
seg_quals = [quals[segment[0]: segment[1] + 1]
for segment in get_uppercase_segments(str_seq)]
qual = sum(sum(q) * len(q) for q in seg_quals) / len(quals)
else:
qual = sum(quals) / len(quals)
return True if qual >= self.threshold else False
def _do_check(self, seq):
seq_object = seq.object
try:
quals = seq_object.letter_annotations['phred_quality']
except KeyError:
msg = 'Some of the input sequences do not have qualities: {}'
msg = msg.format(get_name(seq))
raise WrongFormatError(msg)
if self.ignore_masked:
str_seq = str(seq_object.seq)
seg_quals = [quals[segment[0]: segment[1] + 1]
for segment in get_uppercase_segments(str_seq)]
qual = sum(sum(q) * len(q) for q in seg_quals) / len(quals)
else:
qual = sum(quals) / len(quals)
return True if qual >= self.threshold else False
def _do_trim(self, seq):
"It trims the masked segments of the seqrecords."
window = self.window
threshold = self.threshold
trim_left = self.trim_left
trim_right = self.trim_right
try:
quals = list(get_int_qualities(seq))
except KeyError:
msg = "Some of the input sequences do not have qualities: {}"
msg = msg.format(get_name(seq))
segments = _get_bad_quality_segments(quals, window, threshold, trim_left, trim_right)
if segments is not None:
_add_trim_segments(segments, seq, kind=QUALITY)
return seq
def _do_trim(self, seq):
'It trims the masked segments of the seqrecords.'
window = self.window
threshold = self.threshold
trim_left = self.trim_left
trim_right = self.trim_right
try:
quals = list(get_int_qualities(seq))
except KeyError:
msg = 'Some of the input sequences do not have qualities: {}'
msg = msg.format(get_name(seq))
segments = _get_bad_quality_segments(quals, window, threshold,
trim_left, trim_right)
if segments is not None:
_add_trim_segments(segments, seq, kind=QUALITY)
return seq
def __call__(self, seqs):
'It trims the masked segments of the SeqWrappers.'
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 89},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=True)
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
_add_trim_segments(segments[0], seq, kind=VECTOR)
return seqs
def __call__(self, seqs):
'It trims the masked segments of the seqrecords.'
window = self.window
threshold = self.threshold
trim_left = self.trim_left
trim_right = self.trim_right
trimmed_seqs = []
for seq in seqs:
try:
quals = list(get_qualities(seq))
except KeyError:
msg = 'Some of the input sequences do not have qualities: {}'
msg = msg.format(get_name(seq))
segments = _get_bad_quality_segments(quals, window, threshold,
trim_left, trim_right)
if segments is not None:
_add_trim_segments(segments, seq, kind=QUALITY)
trimmed_seqs.append(seq)
return trimmed_seqs
def __call__(self, seqrecords):
'It does the work'
if not seqrecords:
return seqrecords
matcher = Blaster(seqrecords, self.blastdb, self._program,
self._dbtype, filters=self._filters,
params=self._params, remote=self._remote)
blasts = matcher.blasts
blastdb = os.path.basename(self.blastdb)
for seqrecord in seqrecords:
align_result = blasts.get(get_name(seqrecord), None)
if not align_result:
continue
match_counter = 0
for match in align_result['matches']:
subject = match['subject']['name']
match_counter += 1
for match_part in match['match_parts']:
if match_part['subject_end'] < match_part['subject_start']:
strand = -1
subject_start = match_part['subject_end']
subject_end = match_part['subject_start']
else:
strand = 1
subject_start = match_part['subject_start']
subject_end = match_part['subject_end']
query_start = match_part['query_start']
query_end = match_part['query_end']
qualifiers = {}
qualifiers['Target'] = {'start': subject_start,
'end': subject_end,
'name': subject}
qualifiers['score'] = match_part['scores']['expect']
qualifiers['identity'] = match_part['scores']['identity']
qualifiers['blastdb'] = blastdb
location = FeatureLocation(query_start, query_end, strand)
feature = SeqFeature(location=location, type='match_part',
qualifiers=qualifiers,
id='match{0:03d}'.format(match_counter))
seqrecord.object.features.append(feature)
return seqrecords
def _read_estcan_result(fhand, result, file_type):
'It reads a dna or pep ESTscan result file'
for seq in read_seqs([fhand], file_format='fasta'):
items = [i.strip() for i in get_description(seq).split(';')]
strand = -1 if 'minus strand' in items else 1
start, end = items[0].split(' ', 3)[1:3]
# estscan changes the name, we have to fix it
seqid = get_name(seq).strip(';')
try:
seq_orfs = result[seqid]
except KeyError:
seq_orfs = {}
result[seqid] = seq_orfs
orf_key = (int(start), int(end), strand)
if orf_key in seq_orfs:
orf = seq_orfs[orf_key]
else:
orf = {}
seq_orfs[orf_key] = orf
orf[file_type] = get_str_seq(seq)
def _read_estcan_result(fhand, result, file_type):
'It reads a dna or pep ESTscan result file'
for seq in read_seqs([fhand], file_format='fasta'):
items = [i.strip() for i in get_description(seq).split(';')]
strand = -1 if 'minus strand' in items else 1
start, end = items[0].split(' ', 3)[1:3]
# estscan changes the name, we have to fix it
seqid = get_name(seq).strip(';')
try:
seq_orfs = result[seqid]
except KeyError:
seq_orfs = {}
result[seqid] = seq_orfs
orf_key = (int(start), int(end), strand)
if orf_key in seq_orfs:
orf = seq_orfs[orf_key]
else:
orf = {}
seq_orfs[orf_key] = orf
orf[file_type] = get_str_seq(seq)
def _get_chrom_lengths(self):
chrom_lens = OrderedDict()
if self._ref_fhand is None:
vcf_fhand = gzip.open(self._reader.fhand.name)
for line in vcf_fhand:
line = line.strip()
if line.startswith('#'):
continue
items = line.split()
chrom = items[0]
loc = int(items[1])
if chrom not in chrom_lens:
chrom_lens[chrom] = loc
else:
if loc > chrom_lens[chrom]:
chrom_lens[chrom] = loc
else:
for read in read_seqs([self._ref_fhand]):
chrom_lens[get_name(read)] = get_length(read)
return chrom_lens
def _do_trim(self, seq):
'It trims the masked segments of the SeqWrappers.'
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
_add_trim_segments(segments[0], seq, kind=VECTOR)
return seq
def test_classify_paired_reads(self):
reference_seq = GENOME
#Typic non chimeric
query1 = '>seq1 f\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT\n'
query2 = '>seq1 r\nCATCATTGCATAAGTAACACTCAACCAACAGTGCTACAGGGTTGTAACG\n'
#typic chimeric
query3 = '>seq2 f\nAAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGTCTGCGATCCCTG'
query3 += 'GGTAGACTGAGGCCTTCTCGAACTACAAATCATCACCAGACCATGTCCGA\n'
query4 = '>seq2 r\nTTAAGGCACGTACGGTACCTAAATCGGCCTGATGGTATTGATGCTGAACTT'
query4 += 'ATTGCGGCTCACACACCCCTACGTTACACGCAAATGCTGCCCGAAACGTTAT\n'
#PE-like chimera. 5' end does not map
query5 = '>seq3 f\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'
query5 += 'AAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGTCTGCGATCCCTG\n'
query6 = '>seq3 r\nTTAAGGCACGTACGGTACCTAAATCGGCCTGATGGTATTGATGCTGAACTT'
query6 += 'ATTGCGGCTCACACACCCCTACGTTACACGCAAATGCTGCCCGAAACGTTAT\n'
#Non chimeric read fragmented into two different sequences
query7 = '>seq4 f\nCAAATCATCACCAGACCATGTCCGATCCCGGGAGTCTTTTCCAAGGTGTGC'
#first part of f sequence not detected -> unknown instead of mapped
query7 += 'TCTTTATCCGGCCCTTGCTCAAGGGTATGTTAAAACGGCAAGAGCTGCCTGAGCGCG\n'
query8 = '>seq4 r\nTGTTCTGCAATCGATACAACGATCGAATTTAATCTGAGTAACTGCCAATTC'
query8 += 'TGAGTAATATTATAGAAAGT\n'
#Chimeric reads mapping different reference sequence
query9 = '>seq5 f\nTTTATCCGGCCCTTGCTCAAGGGTATGTTAAAACGGCAAGAGCTGC'
query9 += 'CTGAAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGTCTGCGATCCCTGTGG\n'
query10 = '>seq5 r\nACTTATTGCGGCTCACACACCCCTACGTTACACGCAAATGCTGCCCGAAA'
query10 += 'CGTTATCTGCGGTGAAATGATGTTCGCGGAGCTGACTATCGTCGCCTGATGATAAG\n'
query11 = '>seq6 f\nACGCACTGATTGTGCTAGGGCCACAGTAGCGGAGATGATTAAGCAGCGAC'
query11 += 'AACTACAAATCATCACCAGACCATGTCCGATCCCGGGAGTCTTTTCCAAGGTGTGC\n'
query12 = '>seq6 r\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'
query12 += 'TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n'
#Unknown, 3' end does not map, impossible to know if it is chimeric
query13 = '>seq7 f\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT'
query13 += 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query14 = '>seq7 r\nATCATTGCATAAGTAACACTCAACCAACAGTGCTACAGGGTTGTAACGCC'
query14 += 'CCTCGAAGGTACCTTTGCCAGACTGGGCTACAGGACACCCAGTCTCCCGGGAGTCT\n'
#chimeric sequences with wrong direction
query15 = '>seq8 f\nTAGGGCCGTCGCCGCATCCACGTTATCGGAAGGGCAACTTCGTCTCTCCA'
query15 += 'ATCAGCTACCGAATTGGGACCTCTACGGGAGTATGGAACGATTGA\n'
query16 = '>seq8 r\nAGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT'
query16 += 'GATGATTTGTAGTTCGAGAAGGCCTCAGTCTACCGCGCCGTGGGTGCCCGATCCCT\n'
#chimeric sequences with wrong direction
query18 = '>seq9 r\nAAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGTCTGCGATCCCT'
query18 += 'GTGGACTTTCTATAATATTACTCAGAATTGGCAGTTACTCAGATTAAATTCG\n'
query17 = '>seq9 f\nGCACACCTTGGAAAAGACTCCCGGGATCGGACATGGTCTGGTGATGATTT'
query17 += 'GTAGTTCGAGAAGGCCTCAGTCTACCGCGCCGTGGGTGCCCGATCCCTCCTCTAGC\n'
#Unknown, wrong relative positions <== = =>
query19 = '>seq10 f\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT'
query19 += '\n'
query20 = '>seq10 r\nATGTAATACGGGCTAGCCGGGGATGCCGACGATTAAACACGCTGTCATA'
query20 += 'GTAGCGTCTTCCTAGGGTTTTCCCCATGGAATCGGTTATCGTGATACGTTAAATTT\n'
#Unknown, wrong relative positions ==> <= =
query21 = '>seq11 f\nAAGTTCAATGTAGCAAGGGTACATGCTGACGAGATGGGTCTGCGATCCC'
query21 += '\n'
query22 = '>seq11 r\nAAATTTAACGTATCACGATAACCGATTCCATGGGGAAAACCCTAGGAAG'
query22 += 'ACGCTACTATGACAGCGTGTTTAATCGTCGGCATCCCCGGCTAGCCCGTATTACAT\n'
forward = query1 + query3 + query5 + query7 + query9 + query11
forward += query13 + query15 + query17 + query19 + query21
reverse = query2 + query4 + query6 + query8 + query10 + query12
reverse += query14 + query16 + query18 + query20 + query22
f_fhand = NamedTemporaryFile()
f_fhand.write(forward)
f_fhand.flush()
r_fhand = NamedTemporaryFile()
r_fhand.write(reverse)
r_fhand.flush()
paired_fpaths = [f_fhand.name, r_fhand.name]
ref_fhand = NamedTemporaryFile()
ref_fhand.write(reference_seq)
ref_fhand.flush()
#Kind is given per pair of mates
bamfile = _sorted_mapped_reads(ref_fhand.name,
paired_fpaths=paired_fpaths)
result = classify_mapped_reads(bamfile, file_format='fasta')
mapped = [['seq1.f', 'seq1.r'], ['seq4.f', 'seq4.r']]
non_contiguous = [['seq2.f', 'seq2.r'], ['seq3.f', 'seq3.r'],
['seq5.f', 'seq5.r'], ['seq6.f', 'seq6.r'],
['seq10.f', 'seq10.r'], ['seq11.f', 'seq11.r'],
['seq8.f', 'seq8.r']]
unknown = [['seq7.f', 'seq7.r'],
['seq9.f', 'seq9.r'], ['seq4.f', 'seq4.r']]
expected = {'non_chimeric': mapped, 'chimera': non_contiguous,
'unknown': unknown}
for pair in result:
try:
names = [get_name(read) for read in pair[0]]
assert names in expected[pair[1]]
except AssertionError:
str_names = ' '.join(names)
msg = str_names + ' not expected to be '
msg += pair[1]
raise AssertionError(msg)
def _do_check(self, seq):
return True if get_name(seq) in self.seq_ids else False
from crumbs.filters import (FilterByLength, FilterById, FilterByQuality,
FilterBlastMatch, FilterDustComplexity,
seq_to_filterpackets, FilterByRpkm, FilterByBam,
FilterBowtie2Match, FilterByFeatureTypes)
from crumbs.utils.bin_utils import BIN_DIR
from crumbs.utils.test_utils import TEST_DATA_DIR
from crumbs.utils.tags import (NUCL, SEQS_FILTERED_OUT, SEQS_PASSED, SEQITEM,
SEQRECORD)
from crumbs.utils.file_utils import TemporaryDir
from crumbs.seq import get_name, get_str_seq, SeqWrapper
from crumbs.mapping import get_or_create_bowtie2_index
from crumbs.seqio import read_seq_packets
_seqs_to_names = lambda seqs: [get_name(s) for pair in seqs for s in pair]
_seqs_to_str_seqs = lambda seqs: [get_str_seq(s) for pai in seqs for s in pai]
class PacketConversionTest(unittest.TestCase):
'It tests the seqs and filter packet conversion'
def test_seqs_to_filter_packets(self):
'It converts seq packets into filter packets'
seqpackets = [['ACT'], ['CTG', 'TTT']]
filter_packets = list(seq_to_filterpackets(iter(seqpackets)))
expected = [[['ACT']], [['CTG'], ['TTT']]]
assert [p[SEQS_PASSED] for p in filter_packets] == expected
assert [p[SEQS_FILTERED_OUT] for p in filter_packets] == [[], []]
def _create_seqrecord(string):
def _do_check(self, seq):
return False if get_name(seq) in self.mapped_reads else True
def _do_check(self, seq):
segments = self._matcher.get_matched_segments(get_name(seq))
return True if segments is None else False
from Bio.SeqFeature import SeqFeature, FeatureLocation
from crumbs.filters import (FilterByLength, FilterById, FilterByQuality,
FilterBlastMatch, FilterBlastShort,
FilterDustComplexity, seq_to_filterpackets,
FilterByRpkm, FilterByBam, FilterAllNs,
FilterBowtie2Match, FilterByFeatureTypes)
from crumbs.utils.bin_utils import BIN_DIR
from crumbs.utils.test_utils import TEST_DATA_DIR
from crumbs.utils.tags import (NUCL, SEQS_FILTERED_OUT, SEQS_PASSED, SEQITEM,
SEQRECORD)
from crumbs.seq import get_name, get_str_seq, SeqWrapper
from crumbs.seqio import read_seq_packets
_seqs_to_names = lambda seqs: [get_name(s) for pair in seqs for s in pair]
_seqs_to_str_seqs = lambda seqs: [get_str_seq(s) for pai in seqs for s in pai]
class PacketConversionTest(unittest.TestCase):
'It tests the seqs and filter packet conversion'
def test_seqs_to_filter_packets(self):
'It converts seq packets into filter packets'
seqpackets = [['ACT'], ['CTG', 'TTT']]
filter_packets = list(seq_to_filterpackets(iter(seqpackets)))
expected = [[('ACT',)], [('CTG',), ('TTT',)]]
assert [p[SEQS_PASSED] for p in filter_packets] == expected
assert [p[SEQS_FILTERED_OUT] for p in filter_packets] == [[], []]
def _create_seqrecord(string):
def _do_check(self, seq):
segments = self._matcher.get_matched_segments(get_name(seq))
return True if segments is None else False
def _do_check(self, seq):
return True if get_name(seq) in self.seq_ids else False
def _do_check(self, seq):
return False if get_name(seq) in self.mapped_reads else True
def _get_seq_lengths(fhand):
return {get_name(seq): get_length(seq) for seq in read_seqs([fhand])}
class MatePairSplitter(object):
'It splits the input sequences with the provided linkers.'
def __init__(self, linkers=None):
'The initiator'
if linkers is None:
linkers = get_setting('LINKERS')
linkers = [SeqItem(str(i), '>%d\n%s\n' % (i, l)) for i, l in enumerate(linkers)]
linkers = assing_kind_to_seqs(SEQITEM, linkers, 'fasta')
self.linkers = list(linkers)
def __call__(self, seqs):
'It splits a list of sequences with the provided linkers'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
min_identity = 87.0
min_len = 13
filters = [{'kind': 'min_length', 'min_num_residues': min_len,
'length_in_query': False, 'filter_match_parts': True},
{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': min_identity}]
matcher = BlasterForFewSubjects(seq_fhand.name, self.linkers,
program='blastn', filters=filters,
params={'task': 'blastn-short'},
elongate_for_global=True,
seqs_type=NUCL)
new_seqs = []
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
split_seqs = self._split_by_mate_linker(seq, segments)
else:
split_seqs = [seq]
for seq in split_seqs:
new_seqs.append(seq)
return new_seqs
def _split_by_mate_linker(self, seq, (segments, is_partial)):
'It splits the seqs using segments'
if not segments:
return [copy_seq(seq)]
elongated_match = is_partial
if len(segments) == 1:
segment_start = segments[0][0]
segment_end = segments[0][1]
seq_end = get_length(seq) - 1
if segment_start == 0:
new_seq = slice_seq(seq, segment_end + 1, None)
return [new_seq]
elif segment_end == seq_end:
new_seq = slice_seq(seq, None, segment_start)
return [new_seq]
elif segment_end > seq_end:
msg = 'The segment ends after the sequence has ended'
raise RuntimeError(msg)
else:
new_seq1 = slice_seq(seq, None, segment_start)
new_seq2 = slice_seq(seq, segment_end + 1, None)
if elongated_match:
name = get_name(seq) + '_pl'
else:
name = get_name(seq)
new_seq1 = copy_seq(new_seq1, name=name + r'\1')
new_seq2 = copy_seq(new_seq2, name=name + r'\2')
return [new_seq1, new_seq2]
else:
seqs = []
counter = 1
seq_start = 0
for segment_start, segment_end in segments:
if segment_start == 0:
continue
new_seq = slice_seq(seq, seq_start, segment_start)
seq_name = get_name(seq) + '_mlc.part{0:d}'.format(counter)
new_seq = copy_seq(new_seq, name=seq_name)
seqs.append(new_seq)
counter += 1
seq_start = segment_end + 1
else:
if segment_end != get_length(seq) + 1:
new_seq = slice_seq(seq, segment_end + 1, None)
name = get_name(seq) + '_mlc.part{0:d}'.format(counter)
new_seq = copy_seq(new_seq, name=name)
seqs.append(new_seq)
return seqs
def _do_trim(self, seq):
'It trims the masked segments of the SeqWrappers.'
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
_add_trim_segments(segments[0], seq, kind=VECTOR)
return seq